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- PDB-4dki: Structural Insights into the Anti- Methicillin-Resistant Staphylo... -

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Basic information

Entry
Database: PDB / ID: 4dki
TitleStructural Insights into the Anti- Methicillin-Resistant Staphylococcus aureus (MRSA) Activity of Ceftobiprole
ComponentsPenicillin-binding protein 2'
KeywordsHYDROLASE/Antibiotic / enzyme / HYDROLASE-Antibiotic complex
Function / homology
Function and homology information


peptidoglycan L,D-transpeptidase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / membrane => GO:0016020 / cell wall organization / response to antibiotic / membrane
Similarity search - Function
NTF2-like; domain 1 / Penicillin-binding protein 2a; domain 3 / NTF2-like N-terminal transpeptidase / NTF2-like N-terminal transpeptidase domain / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein 2a (Domain 2) / Ribosomal Protein L30; Chain: A, / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily ...NTF2-like; domain 1 / Penicillin-binding protein 2a; domain 3 / NTF2-like N-terminal transpeptidase / NTF2-like N-terminal transpeptidase domain / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein 2a (Domain 2) / Ribosomal Protein L30; Chain: A, / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Roll / Alpha-Beta Complex / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BICARBONATE ION / : / Chem-RB6 / Penicillin-binding protein 2 / Penicillin-binding protein 2
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLovering, A.L. / Gretes, M.C. / Strynadka, N.C.J.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural Insights into the Anti-methicillin-resistant Staphylococcus aureus (MRSA) Activity of Ceftobiprole.
Authors: Lovering, A.L. / Gretes, M.C. / Safadi, S.S. / Danel, F. / de Castro, L. / Page, M.G. / Strynadka, N.C.
History
DepositionFeb 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Penicillin-binding protein 2'
B: Penicillin-binding protein 2'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,80019
Polymers147,5552
Non-polymers2,24617
Water70339
1
A: Penicillin-binding protein 2'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,90510
Polymers73,7771
Non-polymers1,1289
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Penicillin-binding protein 2'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8959
Polymers73,7771
Non-polymers1,1188
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-83 kcal/mol
Surface area57620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.847, 103.471, 186.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Penicillin-binding protein 2'


Mass: 73777.250 Da / Num. of mol.: 2 / Fragment: UNP residues 24-668
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: COL / Gene: mecA, SACOL0033 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5HJW3, UniProt: A0A0H2WXF8*PLUS, serine-type D-Ala-D-Ala carboxypeptidase

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Non-polymers , 5 types, 56 molecules

#2: Chemical ChemComp-RB6 / (2R)-2-[(1R)-1-{[(2Z)-2-(5-amino-1,2,4-thiadiazol-3-yl)-2-(hydroxyimino)acetyl]amino}-2-oxoethyl]-5-({2-oxo-1-[(3R)-pyr rolidin-3-yl]-2,5-dihydro-1H-pyrrol-3-yl}methyl)-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid / BAL 9141, bound form / ceftobiprole, bound form


Mass: 536.585 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N8O6S2
#3: Chemical
ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#4: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cd
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20 mg/mL protein, 5 mM NaHCO3, pH 8.0, 150 mM NaCl, soaked in 0.1mM inhibitor in 100 mM Hepes, pH 7.0, 1 M NaCl, 28% (v/v) PEG 550 MME and 16 mM CdCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298KK

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2007
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 2.9→69.27 Å / Num. obs: 32591 / % possible obs: 91.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 75.85 Å2 / Rsym value: 0.07 / Net I/σ(I): 15.9
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 3.3 / Rsym value: 0.248 / % possible all: 63.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
BUSTER2.11.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→53.29 Å / Cor.coef. Fo:Fc: 0.9421 / Cor.coef. Fo:Fc free: 0.8944 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2365 1640 5.04 %RANDOM
Rwork0.1731 ---
obs0.1764 32539 91.78 %-
Displacement parametersBiso mean: 67.49 Å2
Baniso -1Baniso -2Baniso -3
1-3.3475 Å20 Å20 Å2
2---2.781 Å20 Å2
3----0.5665 Å2
Refine analyzeLuzzati coordinate error obs: 0.375 Å
Refinement stepCycle: LAST / Resolution: 2.9→53.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10210 0 99 39 10348
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0110478HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.3114100HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3821SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes375HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1470HARMONIC5
X-RAY DIFFRACTIONt_it10478HARMONIC20
X-RAY DIFFRACTIONt_nbd6SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.74
X-RAY DIFFRACTIONt_other_torsion22.95
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1366SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11854SEMIHARMONIC4
LS refinement shellResolution: 2.9→3 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2471 71 4.47 %
Rwork0.2099 1517 -
all0.2115 1588 -
obs--91.78 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.31780.06080.04320.30580.24774.0799-0.046-0.0044-0.03210.06750.0517-0.00450.71750.2948-0.0057-0.03880.0888-0.0269-0.18470.0152-0.098118.203529.198251.8805
20.8169-0.0399-1.11090.7060.19742.36410.1110.0550.05120.0636-0.08880.251-0.2033-0.2568-0.0223-0.17610.0339-0.029-0.17910.0301-0.0635-7.408447.082543.5364
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|25 - A|668 A|701 - A|701 }A25 - 668
2X-RAY DIFFRACTION1{ A|25 - A|668 A|701 - A|701 }A701
3X-RAY DIFFRACTION2{ B|25 - B|668 B|701 - B|701 }B25 - 668
4X-RAY DIFFRACTION2{ B|25 - B|668 B|701 - B|701 }B701

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